MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

@article{Guo2013MitoSeekEM,
  title={MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis},
  author={Yan Guo and Jiang Li and Chung-I Li and Shyr Yu and David C. Samuels},
  journal={Bioinformatics},
  year={2013},
  volume={29 9},
  pages={
          1210-1
        }
}
MOTIVATION Exome capture kits have capture efficiencies that range from 40 to 60%. A significant amount of off-target reads are from the mitochondrial genome. These unintentionally sequenced mitochondrial reads provide unique opportunities to study the mitochondria genome. RESULTS MitoSeek is an open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality… 

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References

SHOWING 1-10 OF 12 REFERENCES
Mitochondrial genomes gleaned from human whole-exome sequencing
TLDR
An overview of the computational strategy and results of mitochondrial sequence extraction and assembly and the hidden value of human whole exome sequencing are provided.
Exome sequencing generates high quality data in non-target regions
TLDR
These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data, and should not be ignored in genetic epidemiology studies.
DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
TLDR
A sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling and is more accurate than array-based platforms at high copy number is developed.
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
TLDR
The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Spectrum of somatic mitochondrial mutations in five cancers
Somatic mtDNA mutations have been reported in some human tumors, but their spectrum in different malignancies and their role in cancer development remain incompletely understood. Here, we describe
The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation.
Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes
TLDR
Genome sequences reveal that a deluge of DNA from organelle DNA has constantly been bombarding the nucleus since the origin of organelles, abolished organelle autonomy and increased nuclear complexity.
The generation of mitochondrial DNA large-scale deletions in human cells
TLDR
It seems possible that replication for class I/II deletions through slipped mispairing between two repeats, and repair mainly for class II/III deletions mediated by mtDNA double-strand breaks work together as a powerful and complementary system to compensate for their defects in the generation of all these deletions.
The effect of strand bias in Illumina short-read sequencing data
TLDR
Extreme strand bias indicates a potential high false-positive rate for SNPs, and it is found that SNPs with low or no strand bias have better overall quality.
...
...